-
1
-
-
33745800293
-
Interpreting the protein language using proteomics
-
Jensen, O. N. Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell. Biol. 2006, 7, 391-403.
-
(2006)
Nat. Rev. Mol. Cell. Biol
, vol.7
, pp. 391-403
-
-
Jensen, O.N.1
-
2
-
-
0034614490
-
Signaling-2000 and beyond
-
Hunter, T. Signaling-2000 and beyond. Cell 2000, 100, 113-127.
-
(2000)
Cell
, vol.100
, pp. 113-127
-
-
Hunter, T.1
-
3
-
-
0035072715
-
A systematic approach to the analysis of protein phosphorylation
-
Zhou, H.; Watts, J. D.; Aebersold, R. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 2001, 19, 375-378.
-
(2001)
Nat. Biotechnol
, vol.19
, pp. 375-378
-
-
Zhou, H.1
Watts, J.D.2
Aebersold, R.3
-
4
-
-
0022541790
-
Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography
-
Andersson, L.; Porath, J. Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal. Biochem. 1986, 154, 250-254.
-
(1986)
Anal. Biochem
, vol.154
, pp. 250-254
-
-
Andersson, L.1
Porath, J.2
-
5
-
-
3242688830
-
Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns
-
Pinkse, M. W. H.; Uitto, P. M.; Hilhorst, M. J.; Ooms, B.; Heck, A. J. R. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 2004, 76, 3935-3943.
-
(2004)
Anal. Chem
, vol.76
, pp. 3935-3943
-
-
Pinkse, M.W.H.1
Uitto, P.M.2
Hilhorst, M.J.3
Ooms, B.4
Heck, A.J.R.5
-
6
-
-
34247325212
-
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
-
Macek, B.; Mijakovic, I.; Olsen, J. V.; Gnad, F.; Kumar, C.; Jensen, P. R.; Mann, M. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 2007, 6, 697-707.
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 697-707
-
-
Macek, B.1
Mijakovic, I.2
Olsen, J.V.3
Gnad, F.4
Kumar, C.5
Jensen, P.R.6
Mann, M.7
-
7
-
-
33847778786
-
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry
-
Chi, A.; Huttenhower, C.; Geer, L. Y.; Coon, J. J.; Syka, J. E. P.; Bai, D. L.; Shabanowitz, J.; Burke, D. J.; Troyanskaya, O. G.; Hunt, D. F. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2193-2198.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, pp. 2193-2198
-
-
Chi, A.1
Huttenhower, C.2
Geer, L.Y.3
Coon, J.J.4
Syka, J.E.P.5
Bai, D.L.6
Shabanowitz, J.7
Burke, D.J.8
Troyanskaya, O.G.9
Hunt, D.F.10
-
8
-
-
33750456519
-
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
-
Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
-
(2006)
Cell
, vol.127
, pp. 635-648
-
-
Olsen, J.V.1
Blagoev, B.2
Gnad, F.3
Macek, B.4
Kumar, C.5
Mortensen, P.6
Mann, M.7
-
9
-
-
33846785485
-
Large-scale phosphorylation analysis of mouse liver
-
Villen, J.; Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1488-1493.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A
, vol.104
, pp. 1488-1493
-
-
Villen, J.1
Beausoleil, S.A.2
Gerber, S.A.3
Gygi, S.P.4
-
10
-
-
33847782587
-
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry
-
Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S.; Pandey, A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U.SA. 2007, 104, 2199-2204.
-
(2007)
Proc. Natl. Acad. Sci. U.SA
, vol.104
, pp. 2199-2204
-
-
Molina, H.1
Horn, D.M.2
Tang, N.3
Mathivanan, S.4
Pandey, A.5
-
11
-
-
34248640306
-
Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis
-
Chitted, B. R.; Peng, Z. Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis. Proteomics 2007, 7, 1473-1500.
-
(2007)
Proteomics
, vol.7
, pp. 1473-1500
-
-
Chitted, B.R.1
Peng, Z.2
-
12
-
-
2642521977
-
Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line
-
Shu, H.; Chen, S.; Bi, Q.; Mumby, M.; Brekken, D. L. Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line. Mol. Cell. Proteomics 2004, 3, 279-286.
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 279-286
-
-
Shu, H.1
Chen, S.2
Bi, Q.3
Mumby, M.4
Brekken, D.L.5
-
13
-
-
33645774163
-
Phosphoproteome analysis of the human mitotic spindle
-
Nousiainen, M.; Sillje, H. H. W.; Sauer, G.; Nigg, E. A.; Korner, R. Phosphoproteome analysis of the human mitotic spindle. Proc. Natl. Acad. Sci. U.S.A. 2006, 703, 5391-5396.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A
, vol.703
, pp. 5391-5396
-
-
Nousiainen, M.1
Sillje, H.H.W.2
Sauer, G.3
Nigg, E.A.4
Korner, R.5
-
14
-
-
33646937404
-
Comprehensive identification of phosphorylation sites in postsynaptic density preparations
-
Trinidad, J. C.; Specht, C. G.; Thalhammer, A.; Schoepfer, R.; Burlingame, A. L. Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol. Cell. Proteomics 2006, 5, 914-922.
-
(2006)
Mol. Cell. Proteomics
, vol.5
, pp. 914-922
-
-
Trinidad, J.C.1
Specht, C.G.2
Thalhammer, A.3
Schoepfer, R.4
Burlingame, A.L.5
-
15
-
-
34247383227
-
Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS
-
Lee, J.; Xu, Y.; Chen, Y.; Sprung, R.; Kim, S. C.; Xie, S.; Zhao, Y. Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol. Cell. Proteomics 2007, 6, 669-676.
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 669-676
-
-
Lee, J.1
Xu, Y.2
Chen, Y.3
Sprung, R.4
Kim, S.C.5
Xie, S.6
Zhao, Y.7
-
16
-
-
0032237775
-
Fragmentation of phosphopeptides in an ion trap mass spectrometer
-
DeGnore, J. P.; Qin, J. Fragmentation of phosphopeptides in an ion trap mass spectrometer. J Am. Soc. Mass Spectrom. 1998, 9, 1175-1188.
-
(1998)
J Am. Soc. Mass Spectrom
, vol.9
, pp. 1175-1188
-
-
DeGnore, J.P.1
Qin, J.2
-
17
-
-
33749853607
-
A probability-based approach for high- throughput protein phosphorylation analysis and site localization
-
Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. A probability-based approach for high- throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 2006, 24, 1285-1292.
-
(2006)
Nat. Biotechnol
, vol.24
, pp. 1285-1292
-
-
Beausoleil, S.A.1
Villen, J.2
Gerber, S.A.3
Rush, J.4
Gygi, S.P.5
-
18
-
-
33847194634
-
Automatic validation of phosphopeptide identifications from tandem mass spectra
-
Lu, B.; Ruse, C.; Xu, T.; Park, S. K.; 3rd Yates, J. Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal. Chem. 2007, 79, 1301-1310.
-
(2007)
Anal. Chem
, vol.79
, pp. 1301-1310
-
-
Lu, B.1
Ruse, C.2
Xu, T.3
Park 3rd, S.K.4
Yates, J.5
-
19
-
-
0027461675
-
2. Dissociation of multiply charged proline-containing proteins from electrospray ionization
-
Loo, J. A.; Edmonds, C. G.; Smith, R. D. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization. Anal. Chem. 1993, 65, 425-438.
-
(1993)
Anal. Chem
, vol.65
, pp. 425-438
-
-
Loo, J.A.1
Edmonds, C.G.2
Smith, R.D.3
-
20
-
-
0000312004
-
Protein sequencing by tandem mass spectrometry
-
Hunt, D. F.; Yates, J. R., III; Shabanowitz, J.; Winston, S.; Hauer, C. R. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A 1986, 83, 6233-6237.
-
(1986)
Proc. Natl. Acad. Sci. U.S.A
, vol.83
, pp. 6233-6237
-
-
Hunt, D.F.1
Yates III, J.R.2
Shabanowitz, J.3
Winston, S.4
Hauer, C.R.5
-
21
-
-
0037317111
-
Intensity-based statistical scorer for tandem mass spectrometry
-
Havilio, M.; Haddad, Y.; Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry. Anal. Chem. 2003, 75, 435-444.
-
(2003)
Anal. Chem
, vol.75
, pp. 435-444
-
-
Havilio, M.1
Haddad, Y.2
Smilansky, Z.3
-
22
-
-
0038034116
-
-
Breci, L. A.; Tabb, D. L.; Yates, J. R.; Wysocki, V. H. Anal. Chem. 2003, 75, 1963-71.
-
(2003)
Anal. Chem
, vol.75
, pp. 1963-1971
-
-
Breci, L.A.1
Tabb, D.L.2
Yates, J.R.3
Wysocki, V.H.4
-
24
-
-
27544511899
-
InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
-
Tanner, S.; Shu, H.; Frank, A.; Wang, L.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
-
(2005)
Anal. Chem
, vol.77
, pp. 4626-4639
-
-
Tanner, S.1
Shu, H.2
Frank, A.3
Wang, L.4
Zandi, E.5
Mumby, M.6
Pevzner, P.A.7
Bafna, V.8
-
25
-
-
34547499407
-
Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases
-
Smolka, M. B.; Albuquerque, C. P.; Chen, S.; Zhou, H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc. Natl. Acad. Sci. U.SA. 2007, 104, 10364-10369.
-
(2007)
Proc. Natl. Acad. Sci. U.SA
, vol.104
, pp. 10364-10369
-
-
Smolka, M.B.1
Albuquerque, C.P.2
Chen, S.3
Zhou, H.4
-
26
-
-
0000857494
-
An approach to correlate tandem mass-spectral data of peptides with amino acid sequences in a protein database
-
Eng, J. K.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass-spectral data of peptides with amino acid sequences in a protein database. J Am. Soc. Mass Spectrom. 1994, 5, 976-989.
-
(1994)
J Am. Soc. Mass Spectrom
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
27
-
-
0032750293
-
De novo peptide sequencing via tandem mass spectrometry
-
Dancík, V.; Addona, T. A.; Clauser, K. R.; Vath, J. E.; Pevzner, P. A. De novo peptide sequencing via tandem mass spectrometry. J Comput. Biol. 1999, 6, 327-342.
-
(1999)
J Comput. Biol
, vol.6
, pp. 327-342
-
-
Dancík, V.1
Addona, T.A.2
Clauser, K.R.3
Vath, J.E.4
Pevzner, P.A.5
-
28
-
-
33645235084
-
Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra
-
Venable, J. D.; Xu, T.; Cociorva, D.; Yates, J. R., III. Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal. Chem. 2006, 78, 1921-1929.
-
(2006)
Anal. Chem
, vol.78
, pp. 1921-1929
-
-
Venable, J.D.1
Xu, T.2
Cociorva, D.3
Yates III, J.R.4
-
29
-
-
26844432728
-
Peptide charge state determination for low-resolution tandem mass spectra
-
Klammer, A. A.; Wu, C. C.; MacCoss, M. J.; Noble, W. S. Peptide charge state determination for low-resolution tandem mass spectra. Proc. IEEE Comput. Syst. Bioinform. Conf. 2005, 175-185.
-
(2005)
Proc. IEEE Comput. Syst. Bioinform. Conf
, pp. 175-185
-
-
Klammer, A.A.1
Wu, C.C.2
MacCoss, M.J.3
Noble, W.S.4
-
30
-
-
33845703344
-
What is a support vector machine
-
Noble, W. S. What is a support vector machine. Nat. Biotechnol. 2006, 24, 1565-1567.
-
(2006)
Nat. Biotechnol
, vol.24
, pp. 1565-1567
-
-
Noble, W.S.1
-
32
-
-
33746930864
-
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
-
Keller, A.; Eng, J.; Zhang, N.; Li, X.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 2005-0017.
-
(2005)
Mol. Syst. Biol
, vol.1
, pp. 2005-0017
-
-
Keller, A.1
Eng, J.2
Zhang, N.3
Li, X.4
Aebersold, R.5
-
33
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
34
-
-
24044513966
-
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
-
Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2, 667-675.
-
(2005)
Nat. Methods
, vol.2
, pp. 667-675
-
-
Elias, J.E.1
Haas, W.2
Faherty, B.K.3
Gygi, S.P.4
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